Yea, it was canceled, actually. It stayed canceled for years. One day sharing a cab Iwata brought it up to Itoi and said he really didn't want to see it go to waste, why not start over on GBA? Itoi liked the idea of being able to work with 2D again, as the team's struggles with the third dimension were largely blamed for the constant delays of EB64, and he liked the idea of being able to play on the go in quick sessions (hence the overabundance of save frogs). So if you are a Mother fan and ever find yourself scoffing at Iwata for something stupid like wasting our precious E3 time with the Vitality Sensor, remember that he is the reason Mother 3 finally did get made. ...but that's no reason to stop hating Reggie for not trying harder to get the game localized.

All the information we have lines up surprisingly close with Mother 3, actually. The only thing I don't remember from M3 is the mine cart chase. What are you thinking of that's so different? The same basic plot is there. Porky and the pigmasks. Flint, Hinawa, and the twins. Dragos. The band. Chimeras. Lots of the same locations shown for the most part.

Kumatora was a bit skankier though.

(My goodness that is one of the worst screenshots of the game, which otherwise doesn't look quite so bad.)

I never heard anything about Flint having a bigger role in the 64 version. That is indeed a shame. I, obviously, quite liked his character. His role in the story for Mother 3 is really touching though, so I think it worked out. The only real regrettable part of EB64's eventual conversion into M3 is that we would have gotten Earthbound 64 in the US, if not all the west. :'-(